Multiple sequence alignment - TraesCS5B01G169400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G169400 chr5B 100.000 4765 0 0 1 4765 313956191 313960955 0.000000e+00 8800.0
1 TraesCS5B01G169400 chr5B 98.758 966 10 2 3802 4765 459465419 459464454 0.000000e+00 1716.0
2 TraesCS5B01G169400 chr5B 97.420 969 22 3 3798 4764 610007903 610008870 0.000000e+00 1648.0
3 TraesCS5B01G169400 chr5A 95.642 1675 68 5 2138 3810 365092662 365094333 0.000000e+00 2684.0
4 TraesCS5B01G169400 chr5A 91.776 912 40 15 678 1571 365090918 365091812 0.000000e+00 1236.0
5 TraesCS5B01G169400 chr5A 89.400 500 28 16 1655 2130 365092069 365092567 1.470000e-169 606.0
6 TraesCS5B01G169400 chr5D 96.372 1268 35 5 2546 3810 276708544 276709803 0.000000e+00 2076.0
7 TraesCS5B01G169400 chr5D 90.513 917 45 19 669 1571 276706579 276707467 0.000000e+00 1173.0
8 TraesCS5B01G169400 chr5D 91.136 801 44 19 1655 2434 276707728 276708522 0.000000e+00 1061.0
9 TraesCS5B01G169400 chr6B 98.849 956 9 2 3811 4765 320986599 320985645 0.000000e+00 1703.0
10 TraesCS5B01G169400 chr2B 98.534 955 14 0 3811 4765 753011667 753010713 0.000000e+00 1687.0
11 TraesCS5B01G169400 chr2B 97.974 938 18 1 3828 4765 774683208 774684144 0.000000e+00 1626.0
12 TraesCS5B01G169400 chrUn 98.121 958 17 1 3808 4765 434244767 434245723 0.000000e+00 1668.0
13 TraesCS5B01G169400 chrUn 98.121 958 17 1 3808 4765 445486957 445487913 0.000000e+00 1668.0
14 TraesCS5B01G169400 chr3B 97.708 960 21 1 3804 4762 741225673 741226632 0.000000e+00 1650.0
15 TraesCS5B01G169400 chr3B 94.318 88 5 0 40 127 710580504 710580591 8.320000e-28 135.0
16 TraesCS5B01G169400 chr7B 97.592 955 22 1 3811 4765 531805098 531804145 0.000000e+00 1635.0
17 TraesCS5B01G169400 chr7D 81.525 590 79 19 40 616 499905990 499905418 4.350000e-125 459.0
18 TraesCS5B01G169400 chr7D 80.593 371 65 7 251 616 607123030 607123398 3.630000e-71 279.0
19 TraesCS5B01G169400 chr7D 92.982 57 2 1 2 58 131389278 131389224 1.100000e-11 82.4
20 TraesCS5B01G169400 chr3D 80.985 589 80 20 40 616 558622720 558622152 5.660000e-119 438.0
21 TraesCS5B01G169400 chr4D 84.746 354 42 7 144 496 391485777 391486119 1.270000e-90 344.0
22 TraesCS5B01G169400 chr2A 100.000 49 0 0 2 50 368924668 368924620 1.830000e-14 91.6
23 TraesCS5B01G169400 chr2A 92.982 57 2 2 2 58 687787404 687787350 1.100000e-11 82.4
24 TraesCS5B01G169400 chr2A 90.476 63 3 3 2 61 755730534 755730596 3.950000e-11 80.5
25 TraesCS5B01G169400 chr2D 98.000 50 1 0 2 51 613799402 613799451 2.360000e-13 87.9
26 TraesCS5B01G169400 chr6A 96.226 53 1 1 2 54 149013467 149013416 8.500000e-13 86.1
27 TraesCS5B01G169400 chr1B 93.103 58 1 3 2 59 401931821 401931767 1.100000e-11 82.4
28 TraesCS5B01G169400 chr7A 86.842 76 3 6 2 76 542023013 542022944 1.420000e-10 78.7
29 TraesCS5B01G169400 chr4B 87.143 70 4 5 2 71 402196724 402196660 1.840000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G169400 chr5B 313956191 313960955 4764 False 8800.000000 8800 100.000000 1 4765 1 chr5B.!!$F1 4764
1 TraesCS5B01G169400 chr5B 459464454 459465419 965 True 1716.000000 1716 98.758000 3802 4765 1 chr5B.!!$R1 963
2 TraesCS5B01G169400 chr5B 610007903 610008870 967 False 1648.000000 1648 97.420000 3798 4764 1 chr5B.!!$F2 966
3 TraesCS5B01G169400 chr5A 365090918 365094333 3415 False 1508.666667 2684 92.272667 678 3810 3 chr5A.!!$F1 3132
4 TraesCS5B01G169400 chr5D 276706579 276709803 3224 False 1436.666667 2076 92.673667 669 3810 3 chr5D.!!$F1 3141
5 TraesCS5B01G169400 chr6B 320985645 320986599 954 True 1703.000000 1703 98.849000 3811 4765 1 chr6B.!!$R1 954
6 TraesCS5B01G169400 chr2B 753010713 753011667 954 True 1687.000000 1687 98.534000 3811 4765 1 chr2B.!!$R1 954
7 TraesCS5B01G169400 chr2B 774683208 774684144 936 False 1626.000000 1626 97.974000 3828 4765 1 chr2B.!!$F1 937
8 TraesCS5B01G169400 chrUn 434244767 434245723 956 False 1668.000000 1668 98.121000 3808 4765 1 chrUn.!!$F1 957
9 TraesCS5B01G169400 chrUn 445486957 445487913 956 False 1668.000000 1668 98.121000 3808 4765 1 chrUn.!!$F2 957
10 TraesCS5B01G169400 chr3B 741225673 741226632 959 False 1650.000000 1650 97.708000 3804 4762 1 chr3B.!!$F2 958
11 TraesCS5B01G169400 chr7B 531804145 531805098 953 True 1635.000000 1635 97.592000 3811 4765 1 chr7B.!!$R1 954
12 TraesCS5B01G169400 chr7D 499905418 499905990 572 True 459.000000 459 81.525000 40 616 1 chr7D.!!$R2 576
13 TraesCS5B01G169400 chr3D 558622152 558622720 568 True 438.000000 438 80.985000 40 616 1 chr3D.!!$R1 576

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
475 502 0.040870 CCAGATCCGAGTCGACATCG 60.041 60.0 19.5 21.28 39.86 3.84 F
541 568 0.108945 GCATTGCCAGGTCTTTGCTC 60.109 55.0 0.0 0.00 0.00 4.26 F
2070 2338 0.108520 TAAGTCGTCGGGGTTGATGC 60.109 55.0 0.0 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1386 0.891904 TCACTCACCGGATGTCGACA 60.892 55.0 22.48 22.48 42.43 4.35 R
2517 2877 0.243095 GACGTCACCCAGGACTACAC 59.757 60.0 11.55 0.00 35.63 2.90 R
3794 4162 0.313987 GCCCTTTAACAAAGCACGCT 59.686 50.0 0.00 0.00 37.18 5.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.785853 AGACCCCCTACCCGAGAT 58.214 61.111 0.00 0.00 0.00 2.75
18 19 1.542679 AGACCCCCTACCCGAGATC 59.457 63.158 0.00 0.00 0.00 2.75
19 20 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
20 21 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
21 22 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
22 23 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
23 24 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
24 25 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
25 26 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
27 28 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
28 29 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
29 30 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
30 31 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
31 32 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
32 33 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
33 34 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
34 35 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
71 72 3.302347 CTCGCCAGAAACGCCCTCT 62.302 63.158 0.00 0.00 0.00 3.69
117 118 2.185350 CACCTGGCCAGTAGCTCG 59.815 66.667 30.63 16.73 43.05 5.03
176 194 2.203788 TTCGCCAGGACCACCTCT 60.204 61.111 0.00 0.00 45.94 3.69
177 195 2.232298 CTTCGCCAGGACCACCTCTC 62.232 65.000 0.00 0.00 45.94 3.20
178 196 3.775654 CGCCAGGACCACCTCTCC 61.776 72.222 0.00 0.00 45.94 3.71
179 197 2.607750 GCCAGGACCACCTCTCCA 60.608 66.667 0.00 0.00 45.94 3.86
180 198 2.960688 GCCAGGACCACCTCTCCAC 61.961 68.421 0.00 0.00 45.94 4.02
181 199 2.294078 CCAGGACCACCTCTCCACC 61.294 68.421 0.00 0.00 45.94 4.61
182 200 1.536418 CAGGACCACCTCTCCACCA 60.536 63.158 0.00 0.00 45.94 4.17
183 201 1.536662 AGGACCACCTCTCCACCAC 60.537 63.158 0.00 0.00 44.13 4.16
184 202 2.657237 GACCACCTCTCCACCACG 59.343 66.667 0.00 0.00 0.00 4.94
185 203 3.591254 GACCACCTCTCCACCACGC 62.591 68.421 0.00 0.00 0.00 5.34
186 204 4.394712 CCACCTCTCCACCACGCC 62.395 72.222 0.00 0.00 0.00 5.68
187 205 3.314331 CACCTCTCCACCACGCCT 61.314 66.667 0.00 0.00 0.00 5.52
188 206 2.997897 ACCTCTCCACCACGCCTC 60.998 66.667 0.00 0.00 0.00 4.70
189 207 3.775654 CCTCTCCACCACGCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
190 208 2.681778 CTCTCCACCACGCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
191 209 2.997315 TCTCCACCACGCCTCCTG 60.997 66.667 0.00 0.00 0.00 3.86
192 210 4.767255 CTCCACCACGCCTCCTGC 62.767 72.222 0.00 0.00 0.00 4.85
221 239 4.308458 CTCGCCGGGGACAACACA 62.308 66.667 18.63 0.00 0.00 3.72
225 243 2.753701 CCGGGGACAACACATCCA 59.246 61.111 0.00 0.00 38.06 3.41
228 246 1.458486 GGGGACAACACATCCACCA 59.542 57.895 0.00 0.00 38.06 4.17
231 249 1.577328 GGACAACACATCCACCAGCG 61.577 60.000 0.00 0.00 36.15 5.18
269 287 1.293498 CAGCAGGGCTACGACAACT 59.707 57.895 0.00 0.00 36.40 3.16
296 314 2.671619 GCCTAACAGCGGCCACAA 60.672 61.111 2.24 0.00 41.73 3.33
323 341 4.864334 CGGCACCCAGATCCAGCC 62.864 72.222 0.00 0.00 41.86 4.85
329 347 2.367377 CCAGATCCAGCCAGGGGA 60.367 66.667 0.00 0.00 39.14 4.81
333 351 2.714768 ATCCAGCCAGGGGATCCT 59.285 61.111 12.58 0.00 41.26 3.24
358 385 1.369692 CAGGCTGTACCAACCGTCA 59.630 57.895 6.28 0.00 43.14 4.35
369 396 4.643387 ACCGTCAAGGCAGCACCC 62.643 66.667 0.00 0.00 46.52 4.61
371 398 4.335647 CGTCAAGGCAGCACCCCT 62.336 66.667 0.00 0.00 40.58 4.79
374 401 4.290622 CAAGGCAGCACCCCTGGT 62.291 66.667 0.00 0.00 42.03 4.00
464 491 2.242113 GCATTAGCAGCCAGATCCG 58.758 57.895 0.00 0.00 41.58 4.18
465 492 0.250038 GCATTAGCAGCCAGATCCGA 60.250 55.000 0.00 0.00 41.58 4.55
466 493 1.793258 CATTAGCAGCCAGATCCGAG 58.207 55.000 0.00 0.00 0.00 4.63
467 494 1.069823 CATTAGCAGCCAGATCCGAGT 59.930 52.381 0.00 0.00 0.00 4.18
468 495 0.747255 TTAGCAGCCAGATCCGAGTC 59.253 55.000 0.00 0.00 0.00 3.36
469 496 1.448119 TAGCAGCCAGATCCGAGTCG 61.448 60.000 5.29 5.29 0.00 4.18
470 497 2.775856 GCAGCCAGATCCGAGTCGA 61.776 63.158 15.64 0.07 0.00 4.20
471 498 1.064946 CAGCCAGATCCGAGTCGAC 59.935 63.158 15.64 7.70 0.00 4.20
472 499 1.378646 AGCCAGATCCGAGTCGACA 60.379 57.895 19.50 0.00 0.00 4.35
473 500 0.753479 AGCCAGATCCGAGTCGACAT 60.753 55.000 19.50 5.30 0.00 3.06
474 501 0.318275 GCCAGATCCGAGTCGACATC 60.318 60.000 19.50 14.41 0.00 3.06
475 502 0.040870 CCAGATCCGAGTCGACATCG 60.041 60.000 19.50 21.28 39.86 3.84
480 507 2.827190 CGAGTCGACATCGGGGGA 60.827 66.667 19.50 0.00 40.29 4.81
481 508 2.412323 CGAGTCGACATCGGGGGAA 61.412 63.158 19.50 0.00 40.29 3.97
482 509 1.437986 GAGTCGACATCGGGGGAAG 59.562 63.158 19.50 0.00 40.29 3.46
483 510 2.017559 GAGTCGACATCGGGGGAAGG 62.018 65.000 19.50 0.00 40.29 3.46
484 511 2.762459 TCGACATCGGGGGAAGGG 60.762 66.667 0.73 0.00 40.29 3.95
485 512 2.762459 CGACATCGGGGGAAGGGA 60.762 66.667 0.00 0.00 35.37 4.20
486 513 2.797278 CGACATCGGGGGAAGGGAG 61.797 68.421 0.00 0.00 35.37 4.30
487 514 1.382695 GACATCGGGGGAAGGGAGA 60.383 63.158 0.00 0.00 0.00 3.71
488 515 1.383248 ACATCGGGGGAAGGGAGAG 60.383 63.158 0.00 0.00 0.00 3.20
489 516 2.143419 CATCGGGGGAAGGGAGAGG 61.143 68.421 0.00 0.00 0.00 3.69
490 517 2.333462 ATCGGGGGAAGGGAGAGGA 61.333 63.158 0.00 0.00 0.00 3.71
491 518 2.319410 ATCGGGGGAAGGGAGAGGAG 62.319 65.000 0.00 0.00 0.00 3.69
492 519 2.770475 GGGGGAAGGGAGAGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
493 520 2.370633 GGGGAAGGGAGAGGAGCT 59.629 66.667 0.00 0.00 0.00 4.09
494 521 2.069430 GGGGAAGGGAGAGGAGCTG 61.069 68.421 0.00 0.00 0.00 4.24
495 522 2.741055 GGGAAGGGAGAGGAGCTGC 61.741 68.421 0.00 0.00 0.00 5.25
496 523 2.498726 GAAGGGAGAGGAGCTGCG 59.501 66.667 0.00 0.00 35.50 5.18
497 524 2.284258 AAGGGAGAGGAGCTGCGT 60.284 61.111 0.00 0.00 35.50 5.24
498 525 2.291457 GAAGGGAGAGGAGCTGCGTC 62.291 65.000 0.00 0.41 35.50 5.19
499 526 4.200283 GGGAGAGGAGCTGCGTCG 62.200 72.222 0.00 0.00 35.50 5.12
500 527 4.200283 GGAGAGGAGCTGCGTCGG 62.200 72.222 0.00 0.00 36.53 4.79
501 528 4.200283 GAGAGGAGCTGCGTCGGG 62.200 72.222 0.00 0.00 36.53 5.14
506 533 4.148825 GAGCTGCGTCGGGGTGAT 62.149 66.667 0.00 0.00 0.00 3.06
507 534 4.457496 AGCTGCGTCGGGGTGATG 62.457 66.667 0.00 0.00 36.63 3.07
539 566 4.584688 GCATTGCCAGGTCTTTGC 57.415 55.556 0.00 0.00 0.00 3.68
540 567 1.969862 GCATTGCCAGGTCTTTGCT 59.030 52.632 0.00 0.00 0.00 3.91
541 568 0.108945 GCATTGCCAGGTCTTTGCTC 60.109 55.000 0.00 0.00 0.00 4.26
542 569 0.529378 CATTGCCAGGTCTTTGCTCC 59.471 55.000 0.00 0.00 0.00 4.70
543 570 0.962356 ATTGCCAGGTCTTTGCTCCG 60.962 55.000 0.00 0.00 0.00 4.63
544 571 3.435186 GCCAGGTCTTTGCTCCGC 61.435 66.667 0.00 0.00 0.00 5.54
545 572 2.032528 CCAGGTCTTTGCTCCGCA 59.967 61.111 0.00 0.00 36.47 5.69
553 580 4.675161 TTGCTCCGCAATGGCCCA 62.675 61.111 0.00 0.00 43.99 5.36
554 581 3.961225 TTGCTCCGCAATGGCCCAT 62.961 57.895 0.00 0.00 43.99 4.00
555 582 3.908081 GCTCCGCAATGGCCCATG 61.908 66.667 0.00 0.00 37.80 3.66
556 583 3.221389 CTCCGCAATGGCCCATGG 61.221 66.667 4.14 4.14 37.80 3.66
581 608 4.798682 GAGGGAGGAAGGCGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
582 609 4.348495 AGGGAGGAAGGCGGGGAA 62.348 66.667 0.00 0.00 0.00 3.97
583 610 3.798511 GGGAGGAAGGCGGGGAAG 61.799 72.222 0.00 0.00 0.00 3.46
584 611 3.798511 GGAGGAAGGCGGGGAAGG 61.799 72.222 0.00 0.00 0.00 3.46
585 612 3.798511 GAGGAAGGCGGGGAAGGG 61.799 72.222 0.00 0.00 0.00 3.95
588 615 4.111053 GAAGGCGGGGAAGGGGAC 62.111 72.222 0.00 0.00 0.00 4.46
610 637 2.939353 GGTGGGGGTGCTAGGGTT 60.939 66.667 0.00 0.00 0.00 4.11
611 638 2.544745 GGTGGGGGTGCTAGGGTTT 61.545 63.158 0.00 0.00 0.00 3.27
612 639 1.001269 GTGGGGGTGCTAGGGTTTC 60.001 63.158 0.00 0.00 0.00 2.78
613 640 2.235761 TGGGGGTGCTAGGGTTTCC 61.236 63.158 0.00 0.00 0.00 3.13
614 641 2.681591 GGGGTGCTAGGGTTTCCC 59.318 66.667 0.00 0.00 45.90 3.97
624 651 2.669240 GGTTTCCCCAGGGAGTCG 59.331 66.667 7.25 0.00 46.06 4.18
625 652 2.669240 GTTTCCCCAGGGAGTCGG 59.331 66.667 7.25 0.00 46.06 4.79
626 653 2.609610 TTTCCCCAGGGAGTCGGG 60.610 66.667 7.25 0.00 46.06 5.14
627 654 3.182717 TTTCCCCAGGGAGTCGGGA 62.183 63.158 7.25 1.46 46.34 5.14
628 655 3.618855 TTCCCCAGGGAGTCGGGAG 62.619 68.421 7.25 0.00 46.53 4.30
630 657 4.075793 CCCAGGGAGTCGGGAGGA 62.076 72.222 0.00 0.00 46.34 3.71
631 658 2.038975 CCAGGGAGTCGGGAGGAA 59.961 66.667 0.00 0.00 32.04 3.36
632 659 2.060980 CCAGGGAGTCGGGAGGAAG 61.061 68.421 0.00 0.00 32.04 3.46
633 660 1.000486 CAGGGAGTCGGGAGGAAGA 60.000 63.158 0.00 0.00 0.00 2.87
634 661 0.614979 CAGGGAGTCGGGAGGAAGAA 60.615 60.000 0.00 0.00 0.00 2.52
635 662 0.324830 AGGGAGTCGGGAGGAAGAAG 60.325 60.000 0.00 0.00 0.00 2.85
636 663 1.331399 GGGAGTCGGGAGGAAGAAGG 61.331 65.000 0.00 0.00 0.00 3.46
637 664 1.331399 GGAGTCGGGAGGAAGAAGGG 61.331 65.000 0.00 0.00 0.00 3.95
638 665 1.306226 AGTCGGGAGGAAGAAGGGG 60.306 63.158 0.00 0.00 0.00 4.79
639 666 1.305887 GTCGGGAGGAAGAAGGGGA 60.306 63.158 0.00 0.00 0.00 4.81
640 667 0.908180 GTCGGGAGGAAGAAGGGGAA 60.908 60.000 0.00 0.00 0.00 3.97
641 668 0.178885 TCGGGAGGAAGAAGGGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
642 669 0.253327 CGGGAGGAAGAAGGGGAAAG 59.747 60.000 0.00 0.00 0.00 2.62
643 670 1.373536 GGGAGGAAGAAGGGGAAAGT 58.626 55.000 0.00 0.00 0.00 2.66
644 671 1.004862 GGGAGGAAGAAGGGGAAAGTG 59.995 57.143 0.00 0.00 0.00 3.16
645 672 1.614583 GGAGGAAGAAGGGGAAAGTGC 60.615 57.143 0.00 0.00 0.00 4.40
646 673 1.352687 GAGGAAGAAGGGGAAAGTGCT 59.647 52.381 0.00 0.00 0.00 4.40
647 674 1.074566 AGGAAGAAGGGGAAAGTGCTG 59.925 52.381 0.00 0.00 0.00 4.41
648 675 1.539157 GAAGAAGGGGAAAGTGCTGG 58.461 55.000 0.00 0.00 0.00 4.85
649 676 0.113190 AAGAAGGGGAAAGTGCTGGG 59.887 55.000 0.00 0.00 0.00 4.45
650 677 1.068352 AGAAGGGGAAAGTGCTGGGT 61.068 55.000 0.00 0.00 0.00 4.51
651 678 0.609406 GAAGGGGAAAGTGCTGGGTC 60.609 60.000 0.00 0.00 0.00 4.46
652 679 1.068352 AAGGGGAAAGTGCTGGGTCT 61.068 55.000 0.00 0.00 0.00 3.85
653 680 1.002011 GGGGAAAGTGCTGGGTCTC 60.002 63.158 0.00 0.00 0.00 3.36
654 681 1.761174 GGGAAAGTGCTGGGTCTCA 59.239 57.895 0.00 0.00 0.00 3.27
655 682 0.606673 GGGAAAGTGCTGGGTCTCAC 60.607 60.000 0.00 0.00 0.00 3.51
656 683 0.606673 GGAAAGTGCTGGGTCTCACC 60.607 60.000 0.00 0.00 37.60 4.02
657 684 0.951040 GAAAGTGCTGGGTCTCACCG 60.951 60.000 0.00 0.00 39.83 4.94
658 685 2.397413 AAAGTGCTGGGTCTCACCGG 62.397 60.000 0.00 0.00 39.83 5.28
664 691 4.699522 GGGTCTCACCGGCGCTTT 62.700 66.667 7.64 0.00 39.83 3.51
665 692 3.119096 GGTCTCACCGGCGCTTTC 61.119 66.667 7.64 0.00 0.00 2.62
666 693 3.479269 GTCTCACCGGCGCTTTCG 61.479 66.667 7.64 1.64 39.07 3.46
667 694 3.986006 TCTCACCGGCGCTTTCGT 61.986 61.111 7.64 0.00 38.14 3.85
670 697 2.126228 CACCGGCGCTTTCGTAGA 60.126 61.111 7.64 0.00 38.14 2.59
674 701 1.878522 CGGCGCTTTCGTAGATGCT 60.879 57.895 7.64 0.00 35.04 3.79
705 733 4.237349 GAGTCCTCGATCTTCCAATCTC 57.763 50.000 0.00 0.00 0.00 2.75
706 734 2.962421 AGTCCTCGATCTTCCAATCTCC 59.038 50.000 0.00 0.00 0.00 3.71
707 735 2.695666 GTCCTCGATCTTCCAATCTCCA 59.304 50.000 0.00 0.00 0.00 3.86
708 736 3.133003 GTCCTCGATCTTCCAATCTCCAA 59.867 47.826 0.00 0.00 0.00 3.53
709 737 3.133003 TCCTCGATCTTCCAATCTCCAAC 59.867 47.826 0.00 0.00 0.00 3.77
710 738 3.119291 CTCGATCTTCCAATCTCCAACG 58.881 50.000 0.00 0.00 0.00 4.10
711 739 2.159099 TCGATCTTCCAATCTCCAACGG 60.159 50.000 0.00 0.00 0.00 4.44
713 741 0.984230 TCTTCCAATCTCCAACGGCT 59.016 50.000 0.00 0.00 0.00 5.52
718 746 2.238646 TCCAATCTCCAACGGCTTGTAT 59.761 45.455 0.00 0.00 0.00 2.29
731 759 3.658351 GCTTGTATGCCTACGTCAAAG 57.342 47.619 0.00 0.00 0.00 2.77
755 783 1.922570 CCACGCTCGCACTATTTACT 58.077 50.000 0.00 0.00 0.00 2.24
756 784 2.797087 GCCACGCTCGCACTATTTACTA 60.797 50.000 0.00 0.00 0.00 1.82
757 785 3.639538 CCACGCTCGCACTATTTACTAT 58.360 45.455 0.00 0.00 0.00 2.12
758 786 4.790878 CCACGCTCGCACTATTTACTATA 58.209 43.478 0.00 0.00 0.00 1.31
759 787 4.615961 CCACGCTCGCACTATTTACTATAC 59.384 45.833 0.00 0.00 0.00 1.47
773 801 7.591006 ATTTACTATACCTGACAACGTTGTG 57.409 36.000 36.74 24.36 42.43 3.33
819 847 4.263639 TGCTCCTTTCCTGTGAGATTTCAT 60.264 41.667 0.00 0.00 35.39 2.57
900 938 2.882137 CTCACTATCTTCGTCCTCCTCC 59.118 54.545 0.00 0.00 0.00 4.30
914 959 1.228552 CCTCCCAACCACCACCAAG 60.229 63.158 0.00 0.00 0.00 3.61
915 960 1.536676 CTCCCAACCACCACCAAGT 59.463 57.895 0.00 0.00 0.00 3.16
916 961 0.537371 CTCCCAACCACCACCAAGTC 60.537 60.000 0.00 0.00 0.00 3.01
917 962 1.530655 CCCAACCACCACCAAGTCC 60.531 63.158 0.00 0.00 0.00 3.85
928 973 1.355720 CACCAAGTCCCTCCCAAATCT 59.644 52.381 0.00 0.00 0.00 2.40
963 1008 3.631686 CACAACATCCAAGAAACCACTCA 59.368 43.478 0.00 0.00 0.00 3.41
975 1020 3.052082 CACTCACGGGCAGCTTGG 61.052 66.667 0.00 0.00 0.00 3.61
1454 1500 5.677567 TCTTATTTCGGGATTCCTGTTACC 58.322 41.667 11.35 0.00 0.00 2.85
1459 1505 1.831736 CGGGATTCCTGTTACCTGAGT 59.168 52.381 3.10 0.00 0.00 3.41
1467 1513 4.431378 TCCTGTTACCTGAGTGGGAAATA 58.569 43.478 0.00 0.00 41.09 1.40
1468 1514 4.224370 TCCTGTTACCTGAGTGGGAAATAC 59.776 45.833 0.00 0.00 41.09 1.89
1474 1520 4.848357 ACCTGAGTGGGAAATACAGAATG 58.152 43.478 0.00 0.00 41.17 2.67
1493 1539 9.807649 ACAGAATGCATTATTTGAGGTTATTTC 57.192 29.630 12.97 0.00 42.53 2.17
1499 1545 6.698766 GCATTATTTGAGGTTATTTCTGCTGG 59.301 38.462 0.00 0.00 0.00 4.85
1500 1546 7.416664 GCATTATTTGAGGTTATTTCTGCTGGA 60.417 37.037 0.00 0.00 0.00 3.86
1501 1547 8.469200 CATTATTTGAGGTTATTTCTGCTGGAA 58.531 33.333 0.00 0.00 0.00 3.53
1502 1548 6.916360 ATTTGAGGTTATTTCTGCTGGAAA 57.084 33.333 7.61 7.61 46.33 3.13
1523 1571 2.270874 AATGGGGTCGTGGGATCTGC 62.271 60.000 0.00 0.00 0.00 4.26
1525 1573 2.187946 GGGTCGTGGGATCTGCAG 59.812 66.667 7.63 7.63 0.00 4.41
1526 1574 2.512515 GGTCGTGGGATCTGCAGC 60.513 66.667 9.47 0.00 0.00 5.25
1528 1576 1.520342 GTCGTGGGATCTGCAGCTC 60.520 63.158 9.47 9.27 0.00 4.09
1529 1577 1.984026 TCGTGGGATCTGCAGCTCA 60.984 57.895 18.65 4.83 0.00 4.26
1562 1614 1.742761 ATCTGGTGCCGACTTGATTG 58.257 50.000 0.00 0.00 0.00 2.67
1571 1623 4.744631 GTGCCGACTTGATTGAATTTGTTT 59.255 37.500 0.00 0.00 0.00 2.83
1572 1624 4.981674 TGCCGACTTGATTGAATTTGTTTC 59.018 37.500 0.00 0.00 34.72 2.78
1576 1811 7.148967 GCCGACTTGATTGAATTTGTTTCTAAC 60.149 37.037 0.00 0.00 35.23 2.34
1582 1817 7.526608 TGATTGAATTTGTTTCTAACTAGGCG 58.473 34.615 0.00 0.00 35.23 5.52
1592 1827 4.698583 TCTAACTAGGCGTTCTCTTCAC 57.301 45.455 0.00 0.00 37.05 3.18
1598 1833 3.305398 AGGCGTTCTCTTCACTTGTAG 57.695 47.619 0.00 0.00 0.00 2.74
1627 1871 9.871238 TTCTCTTGAAAATGTAGTATGTACTCC 57.129 33.333 0.00 0.00 37.73 3.85
1632 1876 9.444600 TTGAAAATGTAGTATGTACTCCCTTTC 57.555 33.333 0.00 3.88 37.73 2.62
1640 1884 1.621814 TGTACTCCCTTTCGTTCCTGG 59.378 52.381 0.00 0.00 0.00 4.45
1643 1887 1.772453 ACTCCCTTTCGTTCCTGGAAA 59.228 47.619 11.40 0.00 32.81 3.13
1644 1888 2.173996 ACTCCCTTTCGTTCCTGGAAAA 59.826 45.455 11.40 0.00 33.37 2.29
1645 1889 3.181433 ACTCCCTTTCGTTCCTGGAAAAT 60.181 43.478 11.40 0.00 33.37 1.82
1646 1890 4.042435 ACTCCCTTTCGTTCCTGGAAAATA 59.958 41.667 11.40 0.00 33.37 1.40
1647 1891 5.187621 TCCCTTTCGTTCCTGGAAAATAT 57.812 39.130 11.40 0.00 33.37 1.28
1648 1892 4.947388 TCCCTTTCGTTCCTGGAAAATATG 59.053 41.667 11.40 2.21 33.37 1.78
1649 1893 4.947388 CCCTTTCGTTCCTGGAAAATATGA 59.053 41.667 11.40 0.00 33.37 2.15
1650 1894 5.163652 CCCTTTCGTTCCTGGAAAATATGAC 60.164 44.000 11.40 0.00 33.37 3.06
1651 1895 5.648092 CCTTTCGTTCCTGGAAAATATGACT 59.352 40.000 11.40 0.00 33.37 3.41
1652 1896 6.821665 CCTTTCGTTCCTGGAAAATATGACTA 59.178 38.462 11.40 0.00 33.37 2.59
1653 1897 7.011482 CCTTTCGTTCCTGGAAAATATGACTAG 59.989 40.741 11.40 1.17 33.37 2.57
1672 1916 7.909518 TGACTAGTATTTGCTTTAGGGTACAA 58.090 34.615 0.00 0.00 0.00 2.41
1684 1928 5.625921 TTAGGGTACAATAACGGCAAAAC 57.374 39.130 0.00 0.00 0.00 2.43
1689 1933 3.636282 ACAATAACGGCAAAACCTGTC 57.364 42.857 0.00 0.00 35.61 3.51
1690 1934 2.952978 ACAATAACGGCAAAACCTGTCA 59.047 40.909 0.00 0.00 35.61 3.58
1753 1997 9.443365 AAGTTCTTACTAAGGCTATACCCATAA 57.557 33.333 0.00 0.00 34.31 1.90
1763 2007 5.543020 AGGCTATACCCATAACCTACTTGTC 59.457 44.000 0.00 0.00 40.58 3.18
1781 2025 4.396357 TGTCCCAACCCAAATGATTACT 57.604 40.909 0.00 0.00 0.00 2.24
1803 2047 7.074653 ACTTTTAAGTCCACTGAATCACCTA 57.925 36.000 0.00 0.00 32.86 3.08
1805 2049 6.428083 TTTAAGTCCACTGAATCACCTACA 57.572 37.500 0.00 0.00 0.00 2.74
1806 2050 6.620877 TTAAGTCCACTGAATCACCTACAT 57.379 37.500 0.00 0.00 0.00 2.29
1807 2051 7.727578 TTAAGTCCACTGAATCACCTACATA 57.272 36.000 0.00 0.00 0.00 2.29
1808 2052 5.599999 AGTCCACTGAATCACCTACATAC 57.400 43.478 0.00 0.00 0.00 2.39
1809 2053 5.273208 AGTCCACTGAATCACCTACATACT 58.727 41.667 0.00 0.00 0.00 2.12
1810 2054 5.721960 AGTCCACTGAATCACCTACATACTT 59.278 40.000 0.00 0.00 0.00 2.24
1814 2058 9.429109 TCCACTGAATCACCTACATACTTTATA 57.571 33.333 0.00 0.00 0.00 0.98
1947 2215 4.642885 TGTTGGAACTTGGAAGTACCTTTG 59.357 41.667 0.00 0.00 38.57 2.77
1954 2222 6.796705 ACTTGGAAGTACCTTTGAAATACG 57.203 37.500 0.00 0.00 37.52 3.06
2070 2338 0.108520 TAAGTCGTCGGGGTTGATGC 60.109 55.000 0.00 0.00 0.00 3.91
2108 2376 4.573607 GTCTGATGACATGCTTGCTAATCA 59.426 41.667 0.00 6.02 42.48 2.57
2379 2739 5.710513 TTTTCACTGATCACAGATTTGGG 57.289 39.130 0.00 0.00 46.03 4.12
2407 2767 8.879759 TCAGAAGATTTGCTAATTTAGGTTACG 58.120 33.333 5.61 0.00 0.00 3.18
2417 2777 8.832521 TGCTAATTTAGGTTACGATAATGTTGG 58.167 33.333 5.61 0.00 0.00 3.77
2434 2794 4.009675 TGTTGGACTGAAGTTATGATGGC 58.990 43.478 0.00 0.00 0.00 4.40
2435 2795 2.905075 TGGACTGAAGTTATGATGGCG 58.095 47.619 0.00 0.00 0.00 5.69
2439 2799 3.674997 ACTGAAGTTATGATGGCGTGTT 58.325 40.909 0.00 0.00 0.00 3.32
2454 2814 5.992729 TGGCGTGTTGTAGATAAAAACTTC 58.007 37.500 0.00 0.00 0.00 3.01
2470 2830 7.823745 AAAAACTTCCATGTGTGATAGTCTT 57.176 32.000 0.00 0.00 0.00 3.01
2765 3133 4.804139 GCTAATCTTGCTAGCTACGTGAAA 59.196 41.667 17.23 0.00 38.99 2.69
2795 3163 3.483665 TGCAACGCCGACGCATAC 61.484 61.111 0.00 0.00 45.53 2.39
2801 3169 4.203076 GCCGACGCATACGAGGGT 62.203 66.667 0.00 0.00 43.93 4.34
3062 3430 1.413077 GCTCTGGGTAAACTCGGCTAT 59.587 52.381 0.00 0.00 0.00 2.97
3086 3454 2.620242 CAACTACCCATTGCAATTGGC 58.380 47.619 25.47 0.15 45.13 4.52
3235 3603 4.943705 GTCTGATGTCTATCTTTTTGGCCA 59.056 41.667 0.00 0.00 34.31 5.36
3296 3664 1.201429 AGCGACACTGGGGGATCTTT 61.201 55.000 0.00 0.00 0.00 2.52
3355 3723 2.338500 GTTAGGCAACCGAGTTCTGAG 58.662 52.381 0.00 0.00 37.17 3.35
3701 4069 2.703798 CCATTGCTGCGGGGTCTTG 61.704 63.158 0.00 0.00 0.00 3.02
3723 4091 1.804748 GTGGGGTGTCGATTTTCACTC 59.195 52.381 4.18 0.00 35.26 3.51
3735 4103 3.644966 TTTTCACTCTGTGGGTGTTCT 57.355 42.857 0.00 0.00 36.25 3.01
3761 4129 1.698532 CTTAGGATGATGGGCTCTGCT 59.301 52.381 0.00 0.00 0.00 4.24
3794 4162 1.638070 TGGTCTGTTGGGGCATGATAA 59.362 47.619 0.00 0.00 0.00 1.75
3880 4248 1.381191 TAGCCGTCAGATCAGCCCA 60.381 57.895 0.00 0.00 0.00 5.36
3958 4326 1.502640 CGAGCGTCGTCTTCCTCTT 59.497 57.895 0.00 0.00 34.72 2.85
4753 5126 1.434555 TGCTACAACCGGTTTCATCG 58.565 50.000 19.55 8.74 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.542679 GATCTCGGGTAGGGGGTCT 59.457 63.158 0.00 0.00 0.00 3.85
2 3 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
3 4 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
6 7 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
7 8 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
12 13 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
13 14 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
14 15 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
15 16 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
16 17 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
17 18 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
23 24 0.028374 CGGTTGTCGGTGTCAAAACC 59.972 55.000 0.00 0.00 37.51 3.27
24 25 3.519774 CGGTTGTCGGTGTCAAAAC 57.480 52.632 0.00 0.00 34.75 2.43
71 72 0.739462 CGTTGTGATGGCTCGGCTAA 60.739 55.000 0.00 0.00 0.00 3.09
100 101 2.185350 CGAGCTACTGGCCAGGTG 59.815 66.667 35.42 26.51 43.05 4.00
130 148 1.077357 GGTGTGGTGGTGGTGAACA 60.077 57.895 0.00 0.00 0.00 3.18
133 151 4.555709 GCGGTGTGGTGGTGGTGA 62.556 66.667 0.00 0.00 0.00 4.02
135 153 4.562425 CAGCGGTGTGGTGGTGGT 62.562 66.667 6.41 0.00 42.42 4.16
156 174 2.047179 GGTGGTCCTGGCGAAGAC 60.047 66.667 0.00 0.00 0.00 3.01
204 222 3.605749 ATGTGTTGTCCCCGGCGAG 62.606 63.158 9.30 0.00 0.00 5.03
205 223 3.599285 GATGTGTTGTCCCCGGCGA 62.599 63.158 9.30 0.00 0.00 5.54
206 224 3.124921 GATGTGTTGTCCCCGGCG 61.125 66.667 0.00 0.00 0.00 6.46
207 225 2.750237 GGATGTGTTGTCCCCGGC 60.750 66.667 0.00 0.00 0.00 6.13
217 235 3.952508 TGGCGCTGGTGGATGTGT 61.953 61.111 7.64 0.00 0.00 3.72
219 237 4.722700 GGTGGCGCTGGTGGATGT 62.723 66.667 7.64 0.00 0.00 3.06
221 239 3.731728 ATGGTGGCGCTGGTGGAT 61.732 61.111 7.64 0.00 0.00 3.41
260 278 1.808531 CGTGGTGGGGAGTTGTCGTA 61.809 60.000 0.00 0.00 0.00 3.43
264 282 4.265056 GGCGTGGTGGGGAGTTGT 62.265 66.667 0.00 0.00 0.00 3.32
269 287 2.527123 TGTTAGGCGTGGTGGGGA 60.527 61.111 0.00 0.00 0.00 4.81
308 326 2.124403 CTGGCTGGATCTGGGTGC 60.124 66.667 0.00 0.00 0.00 5.01
312 330 1.773391 ATCCCCTGGCTGGATCTGG 60.773 63.158 12.58 4.57 38.20 3.86
347 374 1.302192 GCTGCCTTGACGGTTGGTA 60.302 57.895 0.00 0.00 34.25 3.25
351 378 2.594592 GGTGCTGCCTTGACGGTT 60.595 61.111 0.00 0.00 34.25 4.44
358 385 3.971702 GACCAGGGGTGCTGCCTT 61.972 66.667 0.00 0.00 35.25 4.35
440 467 3.530067 GGCTGCTAATGCCCTTGG 58.470 61.111 0.00 0.00 44.32 3.61
446 473 0.250038 TCGGATCTGGCTGCTAATGC 60.250 55.000 0.62 0.00 40.20 3.56
447 474 1.069823 ACTCGGATCTGGCTGCTAATG 59.930 52.381 0.62 0.00 0.00 1.90
448 475 1.342819 GACTCGGATCTGGCTGCTAAT 59.657 52.381 0.62 0.00 0.00 1.73
449 476 0.747255 GACTCGGATCTGGCTGCTAA 59.253 55.000 0.62 0.00 0.00 3.09
450 477 1.448119 CGACTCGGATCTGGCTGCTA 61.448 60.000 0.62 0.00 0.00 3.49
451 478 2.780094 CGACTCGGATCTGGCTGCT 61.780 63.158 0.62 0.00 0.00 4.24
452 479 2.279120 CGACTCGGATCTGGCTGC 60.279 66.667 0.62 0.00 0.00 5.25
453 480 1.064946 GTCGACTCGGATCTGGCTG 59.935 63.158 8.70 0.00 0.00 4.85
454 481 0.753479 ATGTCGACTCGGATCTGGCT 60.753 55.000 17.92 0.00 0.00 4.75
455 482 0.318275 GATGTCGACTCGGATCTGGC 60.318 60.000 17.92 0.00 0.00 4.85
456 483 0.040870 CGATGTCGACTCGGATCTGG 60.041 60.000 21.86 0.00 43.02 3.86
457 484 3.446365 CGATGTCGACTCGGATCTG 57.554 57.895 21.86 0.00 43.02 2.90
463 490 2.337749 CTTCCCCCGATGTCGACTCG 62.338 65.000 22.35 22.35 43.02 4.18
464 491 1.437986 CTTCCCCCGATGTCGACTC 59.562 63.158 17.92 10.63 43.02 3.36
465 492 2.058595 CCTTCCCCCGATGTCGACT 61.059 63.158 17.92 1.84 43.02 4.18
466 493 2.499685 CCTTCCCCCGATGTCGAC 59.500 66.667 9.11 9.11 43.02 4.20
467 494 2.762459 CCCTTCCCCCGATGTCGA 60.762 66.667 3.62 0.00 43.02 4.20
468 495 2.762459 TCCCTTCCCCCGATGTCG 60.762 66.667 0.00 0.00 39.44 4.35
469 496 1.382695 TCTCCCTTCCCCCGATGTC 60.383 63.158 0.00 0.00 0.00 3.06
470 497 1.383248 CTCTCCCTTCCCCCGATGT 60.383 63.158 0.00 0.00 0.00 3.06
471 498 2.143419 CCTCTCCCTTCCCCCGATG 61.143 68.421 0.00 0.00 0.00 3.84
472 499 2.287251 CCTCTCCCTTCCCCCGAT 59.713 66.667 0.00 0.00 0.00 4.18
473 500 2.950638 TCCTCTCCCTTCCCCCGA 60.951 66.667 0.00 0.00 0.00 5.14
474 501 2.444895 CTCCTCTCCCTTCCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
475 502 2.770475 GCTCCTCTCCCTTCCCCC 60.770 72.222 0.00 0.00 0.00 5.40
476 503 2.069430 CAGCTCCTCTCCCTTCCCC 61.069 68.421 0.00 0.00 0.00 4.81
477 504 2.741055 GCAGCTCCTCTCCCTTCCC 61.741 68.421 0.00 0.00 0.00 3.97
478 505 2.907236 GCAGCTCCTCTCCCTTCC 59.093 66.667 0.00 0.00 0.00 3.46
479 506 2.291457 GACGCAGCTCCTCTCCCTTC 62.291 65.000 0.00 0.00 0.00 3.46
480 507 2.284258 ACGCAGCTCCTCTCCCTT 60.284 61.111 0.00 0.00 0.00 3.95
481 508 2.757917 GACGCAGCTCCTCTCCCT 60.758 66.667 0.00 0.00 0.00 4.20
482 509 4.200283 CGACGCAGCTCCTCTCCC 62.200 72.222 0.00 0.00 0.00 4.30
483 510 4.200283 CCGACGCAGCTCCTCTCC 62.200 72.222 0.00 0.00 0.00 3.71
484 511 4.200283 CCCGACGCAGCTCCTCTC 62.200 72.222 0.00 0.00 0.00 3.20
489 516 4.148825 ATCACCCCGACGCAGCTC 62.149 66.667 0.00 0.00 0.00 4.09
490 517 4.457496 CATCACCCCGACGCAGCT 62.457 66.667 0.00 0.00 0.00 4.24
522 549 0.108945 GAGCAAAGACCTGGCAATGC 60.109 55.000 0.00 0.00 0.00 3.56
523 550 0.529378 GGAGCAAAGACCTGGCAATG 59.471 55.000 0.00 0.00 0.00 2.82
524 551 0.962356 CGGAGCAAAGACCTGGCAAT 60.962 55.000 0.00 0.00 0.00 3.56
525 552 1.600636 CGGAGCAAAGACCTGGCAA 60.601 57.895 0.00 0.00 0.00 4.52
526 553 2.032528 CGGAGCAAAGACCTGGCA 59.967 61.111 0.00 0.00 0.00 4.92
539 566 3.221389 CCATGGGCCATTGCGGAG 61.221 66.667 18.46 4.08 38.85 4.63
564 591 4.798682 TCCCCGCCTTCCTCCCTC 62.799 72.222 0.00 0.00 0.00 4.30
565 592 4.348495 TTCCCCGCCTTCCTCCCT 62.348 66.667 0.00 0.00 0.00 4.20
566 593 3.798511 CTTCCCCGCCTTCCTCCC 61.799 72.222 0.00 0.00 0.00 4.30
567 594 3.798511 CCTTCCCCGCCTTCCTCC 61.799 72.222 0.00 0.00 0.00 4.30
568 595 3.798511 CCCTTCCCCGCCTTCCTC 61.799 72.222 0.00 0.00 0.00 3.71
571 598 4.111053 GTCCCCTTCCCCGCCTTC 62.111 72.222 0.00 0.00 0.00 3.46
593 620 2.494777 GAAACCCTAGCACCCCCACC 62.495 65.000 0.00 0.00 0.00 4.61
594 621 1.001269 GAAACCCTAGCACCCCCAC 60.001 63.158 0.00 0.00 0.00 4.61
595 622 2.235761 GGAAACCCTAGCACCCCCA 61.236 63.158 0.00 0.00 0.00 4.96
596 623 2.681591 GGAAACCCTAGCACCCCC 59.318 66.667 0.00 0.00 0.00 5.40
608 635 2.669240 CCGACTCCCTGGGGAAAC 59.331 66.667 14.00 5.88 44.66 2.78
609 636 2.609610 CCCGACTCCCTGGGGAAA 60.610 66.667 14.00 0.00 44.66 3.13
610 637 3.607299 TCCCGACTCCCTGGGGAA 61.607 66.667 14.00 0.00 46.81 3.97
614 641 2.038975 TTCCTCCCGACTCCCTGG 59.961 66.667 0.00 0.00 0.00 4.45
615 642 0.614979 TTCTTCCTCCCGACTCCCTG 60.615 60.000 0.00 0.00 0.00 4.45
616 643 0.324830 CTTCTTCCTCCCGACTCCCT 60.325 60.000 0.00 0.00 0.00 4.20
617 644 1.331399 CCTTCTTCCTCCCGACTCCC 61.331 65.000 0.00 0.00 0.00 4.30
618 645 1.331399 CCCTTCTTCCTCCCGACTCC 61.331 65.000 0.00 0.00 0.00 3.85
619 646 1.331399 CCCCTTCTTCCTCCCGACTC 61.331 65.000 0.00 0.00 0.00 3.36
620 647 1.306226 CCCCTTCTTCCTCCCGACT 60.306 63.158 0.00 0.00 0.00 4.18
621 648 0.908180 TTCCCCTTCTTCCTCCCGAC 60.908 60.000 0.00 0.00 0.00 4.79
622 649 0.178885 TTTCCCCTTCTTCCTCCCGA 60.179 55.000 0.00 0.00 0.00 5.14
623 650 0.253327 CTTTCCCCTTCTTCCTCCCG 59.747 60.000 0.00 0.00 0.00 5.14
624 651 1.004862 CACTTTCCCCTTCTTCCTCCC 59.995 57.143 0.00 0.00 0.00 4.30
625 652 1.614583 GCACTTTCCCCTTCTTCCTCC 60.615 57.143 0.00 0.00 0.00 4.30
626 653 1.352687 AGCACTTTCCCCTTCTTCCTC 59.647 52.381 0.00 0.00 0.00 3.71
627 654 1.074566 CAGCACTTTCCCCTTCTTCCT 59.925 52.381 0.00 0.00 0.00 3.36
628 655 1.539157 CAGCACTTTCCCCTTCTTCC 58.461 55.000 0.00 0.00 0.00 3.46
629 656 1.539157 CCAGCACTTTCCCCTTCTTC 58.461 55.000 0.00 0.00 0.00 2.87
630 657 0.113190 CCCAGCACTTTCCCCTTCTT 59.887 55.000 0.00 0.00 0.00 2.52
631 658 1.068352 ACCCAGCACTTTCCCCTTCT 61.068 55.000 0.00 0.00 0.00 2.85
632 659 0.609406 GACCCAGCACTTTCCCCTTC 60.609 60.000 0.00 0.00 0.00 3.46
633 660 1.068352 AGACCCAGCACTTTCCCCTT 61.068 55.000 0.00 0.00 0.00 3.95
634 661 1.464198 AGACCCAGCACTTTCCCCT 60.464 57.895 0.00 0.00 0.00 4.79
635 662 1.002011 GAGACCCAGCACTTTCCCC 60.002 63.158 0.00 0.00 0.00 4.81
636 663 0.606673 GTGAGACCCAGCACTTTCCC 60.607 60.000 0.00 0.00 32.44 3.97
637 664 0.606673 GGTGAGACCCAGCACTTTCC 60.607 60.000 0.00 0.00 42.56 3.13
638 665 0.951040 CGGTGAGACCCAGCACTTTC 60.951 60.000 0.00 0.00 43.15 2.62
639 666 1.071471 CGGTGAGACCCAGCACTTT 59.929 57.895 0.00 0.00 43.15 2.66
640 667 2.743718 CGGTGAGACCCAGCACTT 59.256 61.111 0.00 0.00 43.15 3.16
641 668 3.314331 CCGGTGAGACCCAGCACT 61.314 66.667 0.00 0.00 43.15 4.40
647 674 4.699522 AAAGCGCCGGTGAGACCC 62.700 66.667 21.76 0.00 33.75 4.46
648 675 3.119096 GAAAGCGCCGGTGAGACC 61.119 66.667 21.76 0.00 34.05 3.85
649 676 2.807631 TACGAAAGCGCCGGTGAGAC 62.808 60.000 21.76 0.06 42.48 3.36
650 677 2.537792 CTACGAAAGCGCCGGTGAGA 62.538 60.000 21.76 0.00 42.48 3.27
651 678 2.126228 TACGAAAGCGCCGGTGAG 60.126 61.111 21.76 4.02 42.48 3.51
652 679 1.940883 ATCTACGAAAGCGCCGGTGA 61.941 55.000 21.76 4.04 42.48 4.02
653 680 1.518572 ATCTACGAAAGCGCCGGTG 60.519 57.895 11.67 11.67 42.48 4.94
654 681 1.518572 CATCTACGAAAGCGCCGGT 60.519 57.895 2.29 0.00 42.48 5.28
655 682 2.871427 GCATCTACGAAAGCGCCGG 61.871 63.158 2.29 0.00 42.48 6.13
656 683 1.812214 GAGCATCTACGAAAGCGCCG 61.812 60.000 2.29 2.67 42.48 6.46
657 684 1.927931 GAGCATCTACGAAAGCGCC 59.072 57.895 2.29 0.00 42.48 6.53
670 697 2.168728 GAGGACTCGGGTTTAAGAGCAT 59.831 50.000 0.00 0.00 37.99 3.79
704 732 4.312052 GGCATACAAGCCGTTGGA 57.688 55.556 0.00 0.00 46.12 3.53
711 739 2.223044 GCTTTGACGTAGGCATACAAGC 60.223 50.000 13.32 13.32 33.02 4.01
713 741 2.027561 AGGCTTTGACGTAGGCATACAA 60.028 45.455 9.48 0.00 40.39 2.41
718 746 1.671054 GCAGGCTTTGACGTAGGCA 60.671 57.895 12.32 0.00 40.39 4.75
724 752 4.389576 GCGTGGCAGGCTTTGACG 62.390 66.667 23.77 5.21 37.78 4.35
755 783 6.587226 GTCAATACACAACGTTGTCAGGTATA 59.413 38.462 28.66 18.59 39.91 1.47
756 784 5.407387 GTCAATACACAACGTTGTCAGGTAT 59.593 40.000 30.24 27.36 39.91 2.73
757 785 4.746115 GTCAATACACAACGTTGTCAGGTA 59.254 41.667 30.24 26.51 39.91 3.08
758 786 3.558418 GTCAATACACAACGTTGTCAGGT 59.442 43.478 30.24 25.35 39.91 4.00
759 787 3.059188 GGTCAATACACAACGTTGTCAGG 60.059 47.826 30.24 21.24 39.91 3.86
773 801 5.529060 CAGAGAAGGGCAAATAGGTCAATAC 59.471 44.000 0.00 0.00 0.00 1.89
819 847 1.712056 TCGAGAGTGGAAAAGGTGGA 58.288 50.000 0.00 0.00 0.00 4.02
900 938 1.530655 GGGACTTGGTGGTGGTTGG 60.531 63.158 0.00 0.00 0.00 3.77
914 959 1.153147 GGCGAGATTTGGGAGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
915 960 2.731571 CGGCGAGATTTGGGAGGGA 61.732 63.158 0.00 0.00 0.00 4.20
916 961 2.203070 CGGCGAGATTTGGGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
917 962 2.897350 GCGGCGAGATTTGGGAGG 60.897 66.667 12.98 0.00 0.00 4.30
1341 1386 0.891904 TCACTCACCGGATGTCGACA 60.892 55.000 22.48 22.48 42.43 4.35
1405 1451 4.604843 TGACTGATGCTAAAATGCTTCG 57.395 40.909 0.00 0.00 39.17 3.79
1425 1471 6.488006 ACAGGAATCCCGAAATAAGAATCATG 59.512 38.462 0.00 0.00 37.58 3.07
1454 1500 4.264253 TGCATTCTGTATTTCCCACTCAG 58.736 43.478 0.00 0.00 0.00 3.35
1459 1505 8.303780 TCAAATAATGCATTCTGTATTTCCCA 57.696 30.769 16.86 0.00 34.57 4.37
1467 1513 9.807649 GAAATAACCTCAAATAATGCATTCTGT 57.192 29.630 16.86 0.00 0.00 3.41
1474 1520 6.698766 CCAGCAGAAATAACCTCAAATAATGC 59.301 38.462 0.00 0.00 0.00 3.56
1501 1547 1.357761 AGATCCCACGACCCCATTTTT 59.642 47.619 0.00 0.00 0.00 1.94
1502 1548 0.999712 AGATCCCACGACCCCATTTT 59.000 50.000 0.00 0.00 0.00 1.82
1523 1571 2.276732 TCCCTTTTCCACTTGAGCTG 57.723 50.000 0.00 0.00 0.00 4.24
1525 1573 3.192212 CAGATTCCCTTTTCCACTTGAGC 59.808 47.826 0.00 0.00 0.00 4.26
1526 1574 3.760684 CCAGATTCCCTTTTCCACTTGAG 59.239 47.826 0.00 0.00 0.00 3.02
1528 1576 3.256631 CACCAGATTCCCTTTTCCACTTG 59.743 47.826 0.00 0.00 0.00 3.16
1529 1577 3.500343 CACCAGATTCCCTTTTCCACTT 58.500 45.455 0.00 0.00 0.00 3.16
1562 1614 7.117956 AGAGAACGCCTAGTTAGAAACAAATTC 59.882 37.037 0.00 0.00 44.35 2.17
1571 1623 4.333690 AGTGAAGAGAACGCCTAGTTAGA 58.666 43.478 0.00 0.00 44.35 2.10
1572 1624 4.705337 AGTGAAGAGAACGCCTAGTTAG 57.295 45.455 0.00 0.00 44.35 2.34
1576 1811 3.305398 ACAAGTGAAGAGAACGCCTAG 57.695 47.619 0.00 0.00 0.00 3.02
1582 1817 6.977213 AGAGAAGACTACAAGTGAAGAGAAC 58.023 40.000 0.00 0.00 0.00 3.01
1592 1827 9.482627 ACTACATTTTCAAGAGAAGACTACAAG 57.517 33.333 0.00 0.00 34.71 3.16
1620 1864 1.621814 CCAGGAACGAAAGGGAGTACA 59.378 52.381 0.00 0.00 0.00 2.90
1621 1865 1.897802 TCCAGGAACGAAAGGGAGTAC 59.102 52.381 0.00 0.00 0.00 2.73
1622 1866 2.314071 TCCAGGAACGAAAGGGAGTA 57.686 50.000 0.00 0.00 0.00 2.59
1623 1867 1.430992 TTCCAGGAACGAAAGGGAGT 58.569 50.000 0.00 0.00 0.00 3.85
1627 1871 5.648092 AGTCATATTTTCCAGGAACGAAAGG 59.352 40.000 0.00 0.00 31.22 3.11
1632 1876 8.888579 AATACTAGTCATATTTTCCAGGAACG 57.111 34.615 0.00 0.00 0.00 3.95
1645 1889 9.204337 TGTACCCTAAAGCAAATACTAGTCATA 57.796 33.333 0.00 0.00 0.00 2.15
1646 1890 8.086143 TGTACCCTAAAGCAAATACTAGTCAT 57.914 34.615 0.00 0.00 0.00 3.06
1647 1891 7.484993 TGTACCCTAAAGCAAATACTAGTCA 57.515 36.000 0.00 0.00 0.00 3.41
1648 1892 8.959705 ATTGTACCCTAAAGCAAATACTAGTC 57.040 34.615 0.00 0.00 0.00 2.59
1651 1895 9.316730 CGTTATTGTACCCTAAAGCAAATACTA 57.683 33.333 0.00 0.00 0.00 1.82
1652 1896 7.281549 CCGTTATTGTACCCTAAAGCAAATACT 59.718 37.037 0.00 0.00 0.00 2.12
1653 1897 7.412063 CCGTTATTGTACCCTAAAGCAAATAC 58.588 38.462 0.00 0.00 0.00 1.89
1672 1916 4.864704 AAATGACAGGTTTTGCCGTTAT 57.135 36.364 0.00 0.00 43.70 1.89
1731 1975 7.541967 AGGTTATGGGTATAGCCTTAGTAAGA 58.458 38.462 21.19 2.39 45.10 2.10
1732 1976 7.793948 AGGTTATGGGTATAGCCTTAGTAAG 57.206 40.000 21.19 2.65 45.10 2.34
1763 2007 7.676004 ACTTAAAAGTAATCATTTGGGTTGGG 58.324 34.615 0.00 0.00 37.52 4.12
1781 2025 6.833041 TGTAGGTGATTCAGTGGACTTAAAA 58.167 36.000 0.00 0.00 0.00 1.52
1900 2168 7.942341 ACAACATACTCACCCTCATCTTTAAAA 59.058 33.333 0.00 0.00 0.00 1.52
1969 2237 2.777832 AGAATCCACCTTGACTGAGC 57.222 50.000 0.00 0.00 0.00 4.26
2070 2338 4.520874 TCATCAGACTAAATCTAGGGCTCG 59.479 45.833 0.00 0.00 35.15 5.03
2108 2376 9.965902 AGTAAAGTCTTCAAACAGGATAATGAT 57.034 29.630 0.00 0.00 0.00 2.45
2282 2642 5.645497 GGCACTCAAGTAGAATTTCTGATGT 59.355 40.000 9.22 0.00 0.00 3.06
2342 2702 7.496529 TCAGTGAAAAACAAAGAGTATCCAG 57.503 36.000 0.00 0.00 33.66 3.86
2407 2767 8.562892 CCATCATAACTTCAGTCCAACATTATC 58.437 37.037 0.00 0.00 0.00 1.75
2417 2777 3.262420 ACACGCCATCATAACTTCAGTC 58.738 45.455 0.00 0.00 0.00 3.51
2434 2794 7.533900 CACATGGAAGTTTTTATCTACAACACG 59.466 37.037 0.00 0.00 0.00 4.49
2435 2795 8.349983 ACACATGGAAGTTTTTATCTACAACAC 58.650 33.333 0.00 0.00 0.00 3.32
2439 2799 8.862325 ATCACACATGGAAGTTTTTATCTACA 57.138 30.769 0.00 0.00 0.00 2.74
2454 2814 5.947228 AACACAAAGACTATCACACATGG 57.053 39.130 0.00 0.00 0.00 3.66
2470 2830 9.512435 CATGAAATTTGGCAAATTAAAACACAA 57.488 25.926 31.88 15.22 40.05 3.33
2506 2866 5.726793 ACCCAGGACTACACAGATCTTATTT 59.273 40.000 0.00 0.00 0.00 1.40
2517 2877 0.243095 GACGTCACCCAGGACTACAC 59.757 60.000 11.55 0.00 35.63 2.90
2765 3133 0.524862 CGTTGCACGGGACTACTAGT 59.475 55.000 0.00 0.00 38.08 2.57
3191 3559 2.682494 GGTACACCAGGGCGGAGA 60.682 66.667 0.00 0.00 38.63 3.71
3213 3581 5.178096 TGGCCAAAAAGATAGACATCAGA 57.822 39.130 0.61 0.00 33.21 3.27
3235 3603 4.032310 ACTCTTCTGCTCCTCATCAAGAT 58.968 43.478 0.00 0.00 0.00 2.40
3296 3664 2.601240 TGGCCTGTCCATCAAATGAA 57.399 45.000 3.32 0.00 40.72 2.57
3346 3714 5.115480 CCTCTTTAGCATTCCTCAGAACTC 58.885 45.833 0.00 0.00 33.97 3.01
3347 3715 4.534103 ACCTCTTTAGCATTCCTCAGAACT 59.466 41.667 0.00 0.00 33.97 3.01
3473 3841 1.134580 CACGACCCTCCGTAGTAGAGA 60.135 57.143 0.00 0.00 41.29 3.10
3521 3889 4.207165 AGTAGCTGTTGAAAGCAAAGGAA 58.793 39.130 0.00 0.00 46.08 3.36
3701 4069 1.265905 GTGAAAATCGACACCCCACAC 59.734 52.381 0.00 0.00 0.00 3.82
3723 4091 2.930826 AGGTACAAGAACACCCACAG 57.069 50.000 0.00 0.00 35.25 3.66
3735 4103 3.391296 GAGCCCATCATCCTAAGGTACAA 59.609 47.826 0.00 0.00 0.00 2.41
3761 4129 2.925724 ACAGACCATTTCCAACGTCAA 58.074 42.857 0.00 0.00 0.00 3.18
3794 4162 0.313987 GCCCTTTAACAAAGCACGCT 59.686 50.000 0.00 0.00 37.18 5.07
3805 4173 0.531974 CGCCTAGCATCGCCCTTTAA 60.532 55.000 0.00 0.00 0.00 1.52
3880 4248 4.910585 GATCCAACGGCGCGGGAT 62.911 66.667 26.67 26.67 43.92 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.